High-resolution pore-water and solid-phase analyses of sediment cores GeoB6520-3 (Hydrate Hole) and GeoB6521-2 (Worm Hole) of the northern Congo Fan

The geochemical cycling of barium was investigated in sediments of pockmarks of the northern Congo Fan, characterized by surface and subsurface gas hydrates, chemosynthetic fauna, and authigenic carbonates. Two gravity cores retrieved from the so-called Hydrate Hole and Worm Hole pockmarks were examined using high-resolution pore-water and solid-phase analyses. The results indicate that, although gas hydrates in the study area are stable with respect to pressure and temperature, they are and have been subject to dissolution due to methane-undersaturated pore waters. The process significantly driving dissolution is the anaerobic oxidation of methane (AOM) above the shallowest hydrate-bearing sediment layer. It is suggested that episodic seep events temporarily increase the upward flux of methane, and induce hydrate formation close to the sediment surface. AOM establishes at a sediment depth where the upward flux of methane from the uppermost hydrate layer counterbalances the downward flux of seawater sulfate. After seepage ceases, AOM continues to consume methane at the sulfate/methane transition (SMT) above the hydrates, thereby driving the progressive dissolution of the hydrates "from above". As a result the SMT migrates downward, leaving behind enrichments of authigenic barite and carbonates that typically precipitate at this biogeochemical reaction front. Calculation of the time needed to produce the observed solid-phase barium enrichments above the present-day depths of the SMT served to track the net downward migration of the SMT and to estimate the total time of hydrate dissolution in the recovered sediments. Methane fluxes were higher, and the SMT was located closer to the sediment surface in the past at both sites. Active seepage and hydrate formation are inferred to have occurred only a few thousands of years ago at the Hydrate Hole site. By contrast, AOM-driven hydrate dissolution as a consequence of an overall net decrease in upward methane flux seems to have persisted for a considerably longer time at the Worm Hole site, amounting to a few tens of thousands of years.

Time-resolved dosimetric verification of respiratory-gated radiotherapy exposures using a high-resolution 2D ionisation chamber array

The aim of this work was to track and verify the delivery of respiratory-gated irradiations, performed with three versions of TrueBeam linac, using a novel phantom arrangement that combined the OCTAVIUS® SRS 1000 array with a moving platform. The platform was programmed to generate sinusoidal motion of the array. This motion was tracked using the real-time position management (RPM) system and four amplitude gating options were employed to interrupt MV beam delivery when the platform was not located within set limits. Time-resolved spatial information extracted from analysis of x-ray fluences measured by the array was compared to the programmed motion of the platform and to the trace recorded by the RPM system during the delivery of the x-ray field. Temporal data recorded by the phantom and the RPM system were validated against trajectory log files, recorded by the linac during the irradiation, as well as oscilloscope waveforms recorded from the linac target signal. Gamma analysis was employed to compare time-integrated 2D x-ray dose fluences with theoretical fluences derived from the probability density function for each of the gating settings applied, where gamma criteria of 2%/2 mm, 1%/1 mm and 0.5%/0.5 mm were used to evaluate the limitations of the RPM system. Excellent agreement was observed in the analysis of spatial information extracted from the SRS 1000 array measurements. Comparisons of the average platform position with the expected position indicated absolute deviations of  <0.5 mm for all four gating settings. Differences were observed when comparing time-resolved beam-on data stored in the RPM files and trajectory logs to the true target signal waveforms. Trajectory log files underestimated the cycle time between consecutive beam-on windows by 10.0  ±  0.8 ms. All measured fluences achieved 100% pass-rates using gamma criteria of 2%/2 mm and 50% of the fluences achieved pass-rates  >90% when criteria of 0.5%/0.5 mm were used. Results using this novel phantom arrangement indicate that the RPM system is capable of accurately gating x-ray exposure during the delivery of a fixed-field treatment beam.

High resolution Thomson Parabola Spectrometer for full spectral capture of multi-species ion beams

We report on the experimental characterisation of laser-driven ion beams using a Thomson Parabola Spectrometer (TPS) equipped with trapezoidally shaped electric plates, proposed by Gwynne et al. [Rev. Sci. Instrum. 85, 033304 (2014)]. While a pair of extended (30 cm long) electric plates was able to produce a significant increase in the separation between neighbouring ion species at high energies, deploying a trapezoidal design circumvented the spectral clipping at the low energy end of the ion spectra. The shape of the electric plate was chosen carefully considering, for the given spectrometer configuration, the range of detectable ion energies and species. Analytical tracing of the ion parabolas matches closely with the experimental data, which suggests a minimal effect of fringe fields on the escaping ions close to the wedged edge of the electrode. The analytical formulae were derived considering the relativistic correction required for the high energy ions to be characterised using such spectrometer.

High resolution numerical simulation of triple point collision and origin of unburned gas pockets in turbulent detonations

A key issue in pulse detonation engine development is better understanding of the detonation structure and its propagation mechanism. Thus, in the present work the turbulent structure of an irregular detonation is studied through very high resolution numerical simulations of 600 points per half reaction length. The aim is to explore the nature of the transverse waves during the collision and reflection processes of the triple point with the channel walls. Consequently the formation and consumption mechanism of unreacted gas pockets is studied. Results show that the triple point and the transverse wave collide simultaneously with the wall. The strong transverse wave switches from a primary triple point before collision to a new one after reflection. Due to simultaneous interaction of the triple point and the transverse wave with the wall in the second half of the detonation cell, a larger high-pressurised region appears on the wall. During the reflection the reaction zone detaches from the shock front and produces a pocket of unburned gas. Three mechanisms found to be of significance in the re-initiation mechanism of detonation at the end of the detonation cell; i: energy resealed via consumption of unburned pockets by turbulent mixing ii: compression waves arise due to collision of the triple point on the wall which helps the shock to jump abruptly to an overdriven detonation iii: drastic growth of the Richtmyer–Meshkov instability causing a part of the front to accelerate with respect to the neighbouring portions.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Mapping of Submerged Aquatic Vegetation in Rivers From Very High Resolution Image Data, Using Object Based Image Analysis Combined with Expert Knowledge

The use of remote sensing for monitoring of submerged aquatic vegetation (SAV) in fluvial environments has been limited by the spatial and spectral resolution of available image data. The absorption of light in water also complicates the use of common image analysis methods. This paper presents the results of a study that uses very high resolution (VHR) image data, collected with a Near Infrared sensitive DSLR camera, to map the distribution of SAV species for three sites along the Desselse Nete, a lowland river in Flanders, Belgium. Plant species, including Ranunculus aquatilis L., Callitriche obtusangula Le Gall, Potamogeton natans L., Sparganium emersum L. and Potamogeton crispus L., were classified from the data using Object-Based Image Analysis (OBIA) and expert knowledge. A classification rule set based on a combination of both spectral and structural image variation (e.g. texture and shape) was developed for images from two sites. A comparison of the classifications with manually delineated ground truth maps resulted for both sites in 61% overall accuracy. Application of the rule set to a third validation image, resulted in 53% overall accuracy. These consistent results show promise for species level mapping in such biodiverse environments, but also prompt a discussion on assessment of classification accuracy.

High-resolution image reconstruction from multiple low-resolution images.

In this paper, we demonstrate a digital signal processing (DSP) algorithm for improving spatial resolution of images captured by CMOS cameras. The basic approach is to reconstruct a high resolution (HR) image from a shift-related low resolution (LR) image sequence. The aliasing relationship of Fourier transforms between discrete and continuous images in the frequency domain is used for mapping LR images to a HR image. The method of projection onto convex sets (POCS) is applied to trace the best estimate of pixel matching from the LR images to the reconstructed HR image. Computer simulations and preliminary experimental results have shown that the algorithm works effectively on the application of post-image-captured processing for CMOS cameras. It can also be applied to HR digital image reconstruction, where shift information of the LR image sequence is known.

High resolution mass spectrometry for quantitative analysis and untargeted screening of algal toxins in mussels and passive samplers

Measurement of marine algal toxins has traditionally focussed on shellfish monitoring while, over the last decade, passive sampling has been introduced as a complementary tool for exploratory studies. Since 2011, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been adopted as the EU reference method (No.15/2011) for detection and quantitation of lipophilic toxins. Traditional LC-MS approaches have been based on low-resolution mass spectrometry (LRMS), however, advances in instrument platforms have led to a heightened interest in the use of high-resolution mass spectrometry (HRMS) for toxin detection. This work describes the use of HRMS in combination with passive sampling as a progressive approach to marine algal toxin surveys. Experiments focused on comparison of LRMS and HRMS for determination of a broad range of toxins in shellfish and passive samplers. Matrix effects are an important issue to address in LC-MS; therefore, this phenomenon was evaluated for mussels (Mytilus galloprovincialis) and passive samplers using LRMS (triple quadrupole) and HRMS (quadrupole time-of-flight and Orbitrap) instruments. Matrix-matched calibration solutions containing okadaic acid and dinophysistoxins, pectenotoxin, azaspiracids, yessotoxins, domoic acid, pinnatoxins, gymnodimine A and 13-desmethyl spirolide C were prepared. Similar matrix effects were observed on all instruments types. Most notably, there was ion enhancement for pectenotoxins, okadaic acid/dinophysistoxins on one hand, and ion suppression for yessotoxins on the other. Interestingly, the ion selected for quantitation of PTX2 also influenced the magnitude of matrix effects, with the sodium adduct typically exhibiting less susceptibility to matrix effects than the ammonium adduct. As expected, mussel as a biological matrix, quantitatively produced significantly more matrix effects than passive sampler extracts, irrespective of toxin. Sample dilution was demonstrated as an effective measure to reduce matrix effects for all compounds, and was found to be particularly useful for the non-targeted approach. Limits of detection and method accuracy were comparable between the systems tested, demonstrating the applicability of HRMS as an effective tool for screening and quantitative analysis. HRMS offers the advantage of untargeted analysis, meaning that datasets can be retrospectively analysed. HRMS (full scan) chromatograms of passive samplers yielded significantly less complex data sets than mussels, and were thus more easily screened for unknowns. Consequently, we recommend the use of HRMS in combination with passive sampling for studies investigating emerging or hitherto uncharacterised toxins.

A New Formulation of the Spectral Energy Budget of the Atmosphere, with Application to Two High-Resolution General Circulation Models

International audience

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.